Abstract
Functional magnetic resonance imaging (fMRI) is a brain imaging technology primarily used to investigate how cognitive processes affect neural activity. Due to its non-invasiveness and high spatial resolution, this technology has quickly become one of the most important research tools in cognitive neuroscience and has played a growing role in a number of clinical applications. The interpretation of the results of an fMRI experiment involves the analysis of massive amounts of noisy, complex, multivariate data, resolved both spatially and temporally. The extraction of information from this data is a difficult and articulated task, which relies on methodologies lying at the intersection between image processing, statistics, and machine learning. We here introduce the reader to the rich and diverse literature in the fascinating field of fMRI data analysis, providing an overview of its main challenges and of the most common approaches to overcome them.
Mathematics Subject Classification (2010): Primary 54C40, 14E20, Secondary 46E25, 20C20
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
K.K. Kwong, J.W. Belliveau, D.A. Chesler, I.E. Goldberg, R.M. Weissko, B.P. Poncelet, D.N. Kennedy, B.E. Hoppel, M.S. Cohen, R. Turner, H.M. Cheng, T.J. Brady, B.R. Rosen, Dynamic magnetic resonance imaging of human brain activity during primary sensory stimulation. Proc. Natl. Acad. Sci. (USA) 89, 5675–5679 (1992)
N. Logothetis, A. Wandell, Interpreting the bold signal. Ann. Rev. Physiol. 66, 735–769 (2004)
P. Belin, R. Zatorre, R. Hoge, A. Evans, B. Pike, Event-related fmri of the auditory cortex. NeuroImage 10, 417–429 (1999)
R. Buckner, J. Goodman, M. Burock, M. Rotte, W. Koutstaal, D. Schacter, B. Rosen, A. Dale, Functional-anatomic correlates of object priming in humans revealed by rapid presentation event-related fmri. Neuron 20, 285–296 (1998)
K. Ochsner, A. Bunge, J. Gross, J. Gabrieli, Rethinking feelings: An fmri study of the cognitive regulation of emotion. J. Neurosci. 14, 1215–1229 (2002)
E. Falk, E. Berkman, T. Mann, B. Harrison, M. Lieberman, Predicting persuasion-induced behavior change from the brain. J. Neurosci. 30, 8421–8424 (2010)
A. Sanfey, J. Rilling, J. Aronson, L. Nystrom, J. Cohen, The neural basis of economic decision-making in the ultimatum game. Science 300, 1755–1758 (2003)
J. Sepulcre, H. Liu, T. Talukdar, I. Martincorena, T. Yeo, R. Buckner, The organization of local and distant functional connectivity in the human brain. PLoS Comput. Biol. 6, e1000808 (2010)
H. Whalley, E. Simonotto, S. Flett, I. Marshall, K. Ebmeier, D. Owens, N. Goddard, E. Johnstone, S. Lawrie, fmri correlates of state and trait effects in subjects at genetically enhanced risk of schizophrenia. Brain 127, 478–490 (2004)
G. Honey, E. Pomarol-Clotet, P. Corlett, R. Honey, P. McKenna, E. Bullmore, P. Fletcher, Functional dysconnectivity in schizophrenia associated with attentional modulation of motor function. Brain 128, 2597–2611 (2005)
M. Wengenroth, M. Blatow, J. Guenther, M. Akbar, V. Tronnier, C. Stippich, Diagnostic benefits of presurgical fmri in patients with brain tumours in the primary sensorimotor cortex. Eur. Radiol. 21, 1517–1525 (2011)
R. Marshall, E. Zarahn, L. Alon, B. Minzer, R. Lazar, J. Krakauer, Early imaging correlates of subsequent motor recovery after stroke. Ann. Neurol. 65, 596–602 (2009)
R. Wise, I. Tracey, The role of fmri in drug discovery. J. Magn. Reson. Imag. 23, 862–876 (2006)
D. Borsook, L. Becerra, R. Hargreaves, A role for fmri in optimizing cns drug development. Nat. Rev. Drug Discov. 5, 411–424 (2006)
M. Lindquist, The statistical analysis of fmri data. Stat. Sci. 23, 439–464 (2008)
E. Amaro Jr., G. Barker, Study design in fmri: Basic principles. Brain Cognit. 60, 220–232 (2006)
W. Machielsen, S. Rombouts, F. Barkhof, P. Scheltens, M. Witter, fmri of visual encoding: Reproducibility of activation. Hum. Brain Mapp. 9, 156–164 (2000)
K. Friston, E. Zarahn, O. Josephs, R. Henson, A. Dale, Stochastic designs in event-related fmri. NeuroImage 10, 607–619 (1999)
O. Josephs, R. Turner, K. Friston, Event-related fmri. human brain mapping. Hum. Brain Mapp. 9, 243–257 (1997)
R. Buxton, K. Uludag, D. Dubowitz, T. Liu, Modeling the hemodynamic response to brain activation. NeuroImage 23, S220–S233 (2004)
D. Donaldson, S. Petersen, J. Ollinger, R. Buckner, Dissociating state and item components of recognition memory using fmri. NeuroImage 13, 129–142 (2001)
M. Greicius, K. Supekar, V. Menon, R. Dougherty, Resting-state functional connectivity reflects structural connectivity in the default mode network. Cerebr. Cortex 19, 72–78 (2009)
J.V. Hajnal, R. Myers, A. Oatridge, J.E. Schwieso, I.R. Young, G.M. Bydder, Artifacts due to stimulus correlated motion in functional imaging of the brain. Magn. Reson. Med. 31, 283–291 (1994)
S. Hamdy, D. Mikulis, A. Crawley, S. Xue, H. Lau, S. Henry, N. Diamant, Identifying global anatomical differences: Deformation-based morphometry. Am. J. Phisiol. 277, G219–G225 (1999)
T. Stephan, E. Marx, H. Bruckmann, T. Brandt, M. Dieterich, Lid closure mimics head movement in fmri. Neuroimage 16, 1156–1158 (2002)
D. Abbott, H. Opdam, R. Briellman, G. Jackson, Brief breath holding may confound functional magnetic resonance imaging studies. Hum. Brain Mapp. 24, 284–290 (2005)
X. Hu, T.H. Le, T. Parrish, P. Erhard, Retrospective estimation and correction of physiological fluctuation in functional mri. Magn. Reson. Med. 34, 201–212 (1995)
A. Moelker, P.M.T. Pattynama, Acoustic noise concerns in functional magnetic resonance imaging. Hum. Brain Mapp. 20, 123–141 (2003)
A. Gordon, R. Smith, K. Keramatian, B. Luus, A. Weinberg, J. Smallwood, J. Schooler, K. Christoff, Mind-wandering, awareness, and task performance: An fmri study. Can. J. Exp. Psychol. 61, 210–216 (2007)
J. Ashburner, C. Hutton, R. Frackowiak, I. Johnsrude, C. Price, K. Friston, Identifying global anatomical differences: Deformation-based morphometry. Hum. Brain Mapp. 6, 348–357 (1998)
S.M. Smith, in Preparing fmri Data for Statistical Analysis, ed. by P. Jezzard, P.M. Matthews, S.M. Smith. Functional MRI: An Introduction to Methods (Oxford University Press, Oxford, 2001)
J. Tanabe, D. Miller, J. Tregellas, R. Freedman, F.G. Meyer, Comparison of detrending methods for optimal fmri preprocessing. NeuroImage 15, 902–907 (2002)
M.J. Brammer, in Head Motion and Its Correction, ed. by P. Jezzard, P.M. Matthews, S.M. Smith. Functional MRI: An Introduction to Methods (Oxford University Press, Oxford, 2001)
L. Freire, J.F. Mangin, Motion correction algorithms may create spurious brain activations in the absence of subject motion. NeuroImage 14, 709–722 (2001)
G. Glover, T.-Q. Li, D. Ress, Image-based method for retrospective correction of physiological motion effects in fmri: Retroicor. Magn. Reson. Med. 44, 162–167 (2000)
K.-H. Chuang, J.-H. Chen, Impact: Image-based physiological artifacts estimation and correction technique for functional mri. Magn. Reson. Med. 46, 344–353 (2000)
F. Crivello, T. Schormann, N. Tzourio-Mazoyer, P. Roland, K. Zilles, B. Mazoyer, Comparison of spatial normalization procedures and their impact on functional maps. Hum. Brain Mapp. 16, 228–250 (2002)
J. Talairach, P. Tournoux, Co-Planar Stereotaxic Atlas of the Human Brain (Thieme, New York, 1988)
A. Evans, D. Collins, S. Mills, E. Brown, L. Kelly, T. Peters, in 3d Statistical Neuroanatomical Models from 305 mri Volumes. Proceedings of the IEEE Nuclear Science Symposium and Medical Imaging Conference, vol. 3, pp. 1813–1817 (1993)
P. Fransson, K.-D. an Merboldt, K.M. Petersson, M. Ingvar, J. Frahm, On the effects of spatial filtering: A comparative fmri study of episodic memory encoding at high and low resolution. NeuroImage 16, 977–984 (2002)
G. Aguirre, E. Zarahn, M. D’Esposito, The variability of human, bold hemodynamic responses. NeuroImage 8, 360–369 (1998)
R. Menon, S. Ogawa, J. Strupp, P. Andersen, K. Ugurbil, Bold based functional mri at 4 tesla includes a capillary bed contribution: Echo-planar imaging mirrors previous optical imaging using intrinsic signals. Magn. Reson. Med. 33, 453–459 (1995)
G. Glover, Deconvolution of impulse response in event-related bold fmri. NeuroImage 9, 416–129 (1999)
J. Rajapske, F. Kruggel, J. Maisog, D. Von Cramon, Modeling hemodynamic response for analysis of functional mri time-series. Hum. Brain Mapp. 6, 283–300 (1998)
N. Lazar, The Statistical Analysis of Functional MRI Data (Springer, New York, 2008)
T. Hastie, R. Tibshirani, J. Friedman, The Elements of Statistical Learning: Data Mining, Inference and Prediction (Springer, New York, 2009)
T. Mitchell, R. Hutchinson, R.S. Niculescu, F. Pereira, X. Wang, M. Just, S. Newman, Learning to decode cognitive states from brain images. Mach. Learn. 57, 145–175 (2004)
F. Pereira, T. Mitchell, M. Botvinick, Machine learning classifiers and fmri: A tutorial overview. NeuroImage 45, S199–S209 (2009)
F. Pereira, G. Gordon, in The Support Vector Decomposition Machine. Proceedings of the International Conference on Machine Learning (ICML) (2006)
V. Calhoun, T. Adali, G. Pearlson, J. Pekar, Spatial and temporal independent component analysis of functional mri data containing a pair of task-related waveforms. Hum. Brain Mapp. 13, 43–53 (2001)
Y. Shimizu, M. Barth, C. Windischberger, E. Moser, S. Thurner, Wavelet-based multifractal analysis of fmri time series. Neuroimage 22, 1195–1202 (2004)
C. Neil, H. Trevor, J. Iain, Statistical models for image sequences. Technical report, Stanford University (1998)
N. Lange, S. Zeger, Non-linear fourier time series analysis for human brain mapping by functional magnetic resonance imaging. J. Roy. Stat. Soc. C (Appl. Stat.) 46, 1–29 (1997)
M. Misaki, Y. Kim, P. Bandettini, N. Kriegeskorte, Comparison of multivariate classifiers and response normalizations for pattern-information fmri. Neuroimage 53, 103–118 (2010)
J. Haxby, I. Gobbini, M. Furey, A. Ishai, J. Schouten, P. Pietrini, Distributed and overlapping representations of faces and objects in ventral temporal cortex. Science 293, 2425–2430 (2001)
N. Kriegeskorte, R. Goebel, P. Bandettini, Information-based functional brain mapping. Proc. Natl. Acad. Sci. U.S.A. 103, 3863–3868 (2006)
L.K. Hansen, J. Larsen, F.A. Nielsen, S.C. Strother, E. Rostrup, R. Savoy, N. Lange, J. Sidtis, C. Svarer, O.B. Paulson, Generalizable patterns in neuroimaging: How many principal components? NeuroImage 9, 534–544 (1999)
F. De Martino, F. Gentile, F. Esposito, M. Balsi, F. Di Salle, R. Goebel, E. Formisano, Classification of fmri independent components using ic-fingerprints and support vector machine classifiers. NeuroImage 34, 177–194 (2007)
K. Norman, S. Polyn, G. Detre, J. Haxby, Beyond mind-reading: multi-voxel pattern analysis of fmri data. Trends Cognit. Sci. 10, 424–430 (2006)
S. LaConte, S. Peltier, X. Hu, Real-time fmri using brain-state classification. Hum. Brain Mapp. 28, 1033–1044 (2007)
D. Cox, L. Savoy, Functional magnetic resonance imaging (fmri) ’brain reading’: detecting and classifying distributed patterns of fmri activity in human visual cortex. Neuroimage 19, 261–270 (2003)
X. Wang, R. Hutchinson, T. Mitchell, in Training fmri Classifiers to Detect Cognitive States Across Multiple Human Subjects. NIPS03 (2003)
S. LaConte, S. Strother, V. Cherkassky, J. Anderson, X. Hu, Support vector machines for temporal classification of block design fmri data. NeuroImage 26, 317–329 (2005)
T. Mitchell, R. Hutchinson, M. Just, R. Niculescu, F. Pereira, X. Wang, in Classifying Instantaneous Cognitive States from fmri Data. AMIA Annual Symposium Proceedings, pp. 465–469 (2003)
C. Cortes, V. Vapnik, Support vector networks. Mach. Learn. 20, 273–297 (1995)
S. Ryali, K. Supekar, D.A. Abrams, V. Menon, Sparse logistic regression for whole-brain classification of fmri data. Neuroimage 51, 752–764 (2010)
C. Baudelet, B. Gallez, Cluster analysis of bold fmri time series in tumors to study the heterogeneity of hemodynamic response to treatment. Magn. Reson. Med. 49, 135–145 (2003)
J. Lancaster, M. Woldorff, L. Parsons, M. Liotti, C. Freitas, L. Rainey, P. Kochunov, D. Nickerson, S. Mikiten, P. Fox, Automated talairach atlas labels for functional brain mapping. Hum. Brain Mapp. 10, 120–131 (2000)
R. Heller, D. Stanley, D. Yekutieli, N. Rubin, Y. Benjaminia, Cluster-based analysis of fmri data. Neuroimage 33, 599–608 (2006)
C. Goutte, P. Toft, E. Rostrup, F.A. Nielsen, K.L. Hansen, On clustering fmri time series. Neuroimage 9, 298–310 (1999)
J. Ye, N. Lazar, Y. Li, Geostatistical analysis in clustering fmri time series. Stat. Med. 28, 2490–2508 (2009)
D. Balslev, F.A. Nielsen, S.A. Frutiger, J.J. Sidtis, T.B. Christiansen, C. Svarer, S.C. Strother, D.A. Rottenberg, L.K. Hansen, O.B. Paulson, I. Law, Cluster analysis of activity-time series in motor learning. Hum. Brain Mapp. 15, 135–145 (2002)
M.J. Fadili, S. Ruan, D. Bloyet, B. Mazoyer, A multistep unsupervised fuzzy clustering analysis of fmri time series. Hum. Brain Mapp. 10, 160–178 (2000)
L. Stanberry, R. Nandy, D. Cordes, Cluster analysis of fmri data using dendrogram sharpening. Hum. Brain Mapp. 20, 201–219 (2003)
J. MacQueen, in Some Methods for Classification and Analysis of Multivariate Observations. Proceedings of 5th Berkeley Symposium on Mathematical Statistics and Probability (University of California Press, CA, 1967), pp. 281–297
J. Bezdek, R. Ehrlich, W. Full, Fcm: The fuzzy c-means clustering algorithm. Comp. Geosci. 10, 191–203 (1984)
B. Yeo, W. Ou, Clustering fmri time series. http://people.csail.mit.edu/ythomas/unpublished/6867fMRI.pdf. 2004
P. Filzmoser, R. Baumgartner, E. Moser, A hierarchical clustering method for analyzing functional mr images. Magn. Reson. Imag. 17, 817–826 (1999)
R. Baumgartner, C. Windischberger, E. Moser, Quantification in functional magnetic resonance imaging: Fuzzy clustering vs. correlation analysis. Magn. Reson. Imag. 16, 115–125 (1998)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this chapter
Cite this chapter
Gazzola, G., Chou, CA., Jeong, M.K., Chaovalitwongse, W.A. (2013). An Introduction to the Analysis of Functional Magnetic Resonance Imaging Data. In: Pardalos, P., Coleman, T., Xanthopoulos, P. (eds) Optimization and Data Analysis in Biomedical Informatics. Fields Institute Communications, vol 63. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-4133-5_7
Download citation
DOI: https://doi.org/10.1007/978-1-4614-4133-5_7
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-4132-8
Online ISBN: 978-1-4614-4133-5
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)